title: 2112_2_C0401_T0401

description:
Control (CH1): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25degreesC in night. After growing with deionized water for first 14days, plants were transferred to hydroponic culture medium (Hayashi and chino 1995) without silicic acid (SiO2), and further grown for 14days. Total RNA from shoot of the plants was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25degreesC in night. After growing with deionized water for first 14days, plants were transferred to hydroponic culture medium (Hayashi and chino 1995) with 1ppm SiO2 ,and further grown for 14days. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Silicic acid,

source_name: Control (CH1) source: Plants (shoot) were grown hydroponically, under natural light in a green house without silicic acid, SiO2

source_name: Target (CH2) source: Plant (shoot) treated with 1ppm silicic acid (Si) for 14 days


title: 2118_2_C0002_T0002

status: Public on Aug 13 2009

type: RNA

city: Tsukuba

first: Shoshi

last: Kikuchi

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

description:
Control (CH1): Insertion mutant of WRKY gene from Oryza sativa, Nipponbare (Tos17ID: ND7051) was grown at green house for three-month. The leaf were used for RNA extraction. Messenger RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Insertion mutant of WRKY gene from Oryza sativa, Nipponbare (Tos17ID: ND7051) was grown at green house for three-month.  The plants were incubated for 24 hours on the buffer (0.05%MES/KOH(ph 5.8)) after cutting into sengements. The leaf wounded treatment were used for RNA extraction. Messenger RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, WRKY gene,

molecule: total RNA

organism: Oryza sativa

source_name: Control (CH1) source: Non treated leaf (three-month in the green house) of insertion mutant of WRKY gene

source_name: Target (CH2) source: Insertion mutant of WRKY gene with wounding treatment


title: 2112_2_C0201_T0201

description:
Control (CH1): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25degreesC in night. After growing with deionized water for first 15days, hydroponic culture medium (Hayashi and chino 1995) was used.  At 25days aftrer sowing, plants were transfered to newly prepared normal medium and further grown for 72 hours. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25 degreesC in night. After growing with deionized water for first 15days, hydroponic culture medium (Hayashi and chino 1995) was used.  At 25days aftrer sowing, plants were transfered to the medium in which sulfate ion was replaced with cloride ion, and further grown for 72 hours. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Sulfur,

source_name: Control (CH1) source: Plants (shoot) were grown hydroponically, under natural light in a green house

source_name: Target (CH2) source: Plant (shoot) treated with sulfur (SO4-) defecient condition for 72 hours


title: 2102_1_C0001_T0002

description:
Control (CH1): The japonica rice variety Nipponbare were grown hydrponically for 11-days without treatment. Leaves of plants used for totall RNA extraction by phenol-SDS method. Messenger RNA was purified by oligo(dT) cellulose, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydrponically for 11-days that treated with 0.1M mannitol for 2days. Leaves of plants used for total RNA extraction by phenol-SDS method. Messenger RNA was purified by oligo(dT) cellulose, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Osmotic, ,

source_name: Control (CH1) source: Seedling (leaf) grown hydrponically for 11 days without treatment

source_name: Target (CH2) source: 11-days grown leaves treated with 0.1M mannitol for 2days


title: 2101_1_C0001_T0002

description:
Control (CH1): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with H2O for 5 hours as control plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with low temperature (4 degrees C) for 5hours as target plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: 3 weeks seedlings (whole plant) treated with H2O for 5 hours

source_name: Target (CH2) source: 3 weeks-seedlings treated with 4 degrees C for 5hours


title: 2116_1_C0001_T0002

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) was grown under white fluorescent light (about 600 mol m-2 s-1, 12 h light period/day) at 25 degreesC and 75% relative humidity in a growth chamber. The shoot (above ground parts) was prepared from 1-week-old seedlings. Tissue samples were quick-frozen in liquid nitrogen. Samples were ground to a powder using a mortar and pestle, and total RNAs were isolated according to the procedure described by Chomcyznski and Sacchi (Yang etal. Mol Gen Genomics 2004 271; 468). Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) was grown under white fluorescent light (about 600 mol m-2 s-1, 12 h light period/day) at 25 degreesC and 75% relative humidity in a growth chamber. The shoot (above ground parts) was prepared from 1-week-old seedlings. Lamina joint was treated with 1microM Blasinostreloid for 6 hours. Tissue samples were quick-frozen in liquid nitrogen. Samples were ground to a powder using a mortar and pestle, and total RNAs were isolated according to the procedure described by Chomcyznski and Sacchi (Yang etal. Mol Gen Genomics 2004 271; 468). Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Blasinostreloid,

source_name: Control (CH1) source: Lamina joint segment from one-week-old rice seedling without treatment

source_name: Target (CH2) source: Lamina joint was treated with 1microM Blasinostreloid for 6 hours.


title: 2101_2_C0001_T0002

description:
Control (CH1): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with H2O for 5 hours as control plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with plant hormone, ABA (100 microM) for 5hours as target plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA,

source_name: Target (CH2) source: 3 weeks-whole plants grown under dark condition treated with ABA (100 microM) for 5 hours


title: 2109_2_C0002_T0001

description:
Control (CH1): Seedlings of the japonica rice variety Akitakomachi were grown under submarged condition at 20 degreesC. Coleoptiles at germination stage was harvested for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of the japonica rice variety Akitakomachi were grown under submarged condition at 20 degreesC. And then seedlings was cooled down to 18 degrees. the Coleoptiles of seedlings at germination stage was harvested for RNA extraction. RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Anerobic, Cold,

source_name: Control (CH1) source: Seedling (coleoptile) of submarged rice grown at 20 degreesC

source_name: Target (CH2) source: Seedlings (coleoptiles at germination) of submarged plant grown at 20 degreesC, cooled down to 18 degrees


title: 1000_4_C0001_T0001

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone IAA and cultured for 3 d. The concentration of the plant hormone was adjusted to 100microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, IAA, Callus

source_name: Control (CH1) source: Non treated callus (grown on MS medium including 2.4D for 30 days)

source_name: Target (CH2) source: Callus treated with 100microM IAA for 3 days


title: 2112_1_C0001_T0001

description:
Control (CH1): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25degreesC in night. After growing with deionized water for first 15days, hydroponic culture medium (Hayashi and chino 1995) was used.  At 25days aftrer sowing, plants were transfered to newly prepared normal medium and further grown for 48 hours. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydroponically, under natural light in a green house. It was 30 degreesC in day,  25degreesC in night. After growing with deionized water for first 15days, hydroponic culture medium (Hayashi and chino 1995) was used.  At 25days aftrer sowing, plants were transfered to the medium in which sulfate ion was replaced with cloride ion, and further grown for 48 hours. Total RNA from shoot of the plans was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Sulfur ,

source_name: Control (CH1) source: Plants (shoot) grown hydroponically, under natural light in a green house

source_name: Target (CH2) source: Plant (shoot) treated with sulfur (SO4-) defecient condition for 48 hours


title: 2111_2_C0001_T0004

description:
Control (CH1): The japonica rice variety Michikogane were grown in 1 mM CaCl2 for 2 days at 28 degrees C (24 hours dark) and in 1 mM CaCl2 for 5 days at 28 degrees C (24 hours light). And then, the plants were transfered in standard nutrient solution containing 1 ppm P for 9 days at 28 degrees C (24 hours light). Root at 6 leaves-stage) of the plants used for total RNA extraction by SDS-phenol method (Wasaki et al. Plant, Cell and Environment 2003, 26, 1515). Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Michikogane were grown in 1 mM CaCl2 for 2 days at 28 degrees C (24 hours dark) and in 1 mM CaCl2 for 5 days at 28 degrees C (24 hours light). And then, the plants were transfered in standard nutrient solution containing 1 ppm P for 8 days at 28 degrees C (24 hours light). Finally, the plants were treated with standard nutrient solution without phosphate (phosphate defecient conditions)  for 1 hours at 28 C (24 h light). Root at 6 leaves-stage) of the plants used for total RNA extraction by SDS-phenol method (Wasaki et al. Plant, Cell and Environment 2003, 26, 1515). Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Phosphate,

source_name: Control (CH1) source: Root (6 leaves stage) grown in complete medium containing 1 ppm phosphate

source_name: Target (CH2) source: Plant (root) transferred to phosphate lacking medium and grown 1 hour prior to harvest


title: 2104_1_C0001_T0001

description:
Control (CH1): The japonica rice variety Nipponbare were grown under long day condition (14 hours light 10 hours dark). The full expanded upper leaf was used for toal RNA extraction by RNAgents total RNA isolation system. Messenger RNA was purified by Oligotex-dT30, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown under long day condition (14 hours light 10 hours dark), then transfer and grown into short day condition (10 hours light 14 hours dark) for 5 days. The full expanded upper leaf was used for toal RNA extraction by RNAgents total RNA isolation system. Messenger RNA was purified by Oligotex-dT30, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Day length, ,

source_name: Control (CH1) source: Top leaf grown under long day condition (14 hours light 10 hours dark)

source_name: Target (CH2) source: Plants (full expanded upper leaf) grown under long day condition, then transfer and grown into short day condition for 5 days


title: 1000_6_C0101_T0101

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone Jasmonic acid and cultured for 3 d. The concentration of the plant hormone was adjusted to 50microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Jasmonic acid, Callus

source_name: Target (CH2) source: Callus treated with 50microM Jasmonic acid for 3 days


title: 1000_5_C0001_T0001

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone trans-Zeatin and cultured for 3 d. The concentration of the plant hormone was adjusted to 100microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, trans-Zeatin, Callus

source_name: Target (CH2) source: Callus treated with 100microM trans-Zeatin for 3 days


title: 2110_2_C0101_T0101

description:
Control (CH1): Seedlings of M33 (an acid stress sensitive mutant from the japonica rice variety TaichunT65 donor) germinated under water for two days, then elongation of the seminal root was not inhibited by acid stress pH4.8 for one day, while no crown roots were appeared. M33 was obtained from T65 donor by ion beam mutation method, which seminal root can not elongate at pH4.2 but elongate at pH4.8, the seedlings at two-day stage after the germination were stressed for one day under hydroponics including 10mM MES-NaOH pH4.8, then the seminal root were dissected to isolate the total RNA by Guanidine chloride method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedling of M33 (an acid stress sensitive mutant from the japonica rice variety TaichunT65 donor)  germinated under water for two days, then elongation of the seminal root was inhibited by acid stress pH4.2 for one day, while no crown roots were appeared. M33 was obtained from T65 donor by ion beam mutation method, which seminal root can not elongate at pH4.2 but elongate at pH4.8, the seedlings at two-day stage after the germination were stressed for one day under hydroponics including 10mM MES-NaOH pH4.2, then the seminal root were dissected to isolate the total RNA by Guanidine-chloride method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Acidic pH, Acid stress sensitive mutant,

source_name: Control (CH1) source: Seedling (root) of acid stress sensitive mutant (M33) stressed for one day at pH4.8

source_name: Target (CH2) source: Seminal root of M33 (an acid stress sensitive mutant from Taichung 65) stressed in acidic condition (pH4.2)


title: 2110_1_C0001_T0003

description:
Control (CH1): Seedlings of the japonica rice variety Nipponbare cultured for 2days after onset of the germination in hydroponics including water only. Then the seminal roots were dissected from the seedlings at the sampling stage, no crown roots were observed, for isolate total RNA. Total RNA was extract by using Guanidine chloride method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of the japonica rice variety Nipponbare are cultured for 2days after germination in hydroponics, then are cultured for one day in hydroponics including 10mMMES-NaOH pH5.5. Then the seminal roots were dissected from the seedlings to isolate total RNA by using Guanidine chloride method. Total RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Acidic pH, ,

source_name: Control (CH1) source: Seedling (root) cultured for one day in hydroponics after germination for 2 days

source_name: Target (CH2) source: Seedlings (Nipponbare) were cultured for one day in hydroponics of acidic condition (pH5.5)


title: 2101_1_C0001_T0001

description:
Control (CH1): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with H2O for 5 hours as control plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with 250 mM NaCl for 5 hours as target plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Salt, ,

source_name: Control (CH1) source: 3 weeks seedlings (whole plant) treated with H2O for 5 hours

source_name: Target (CH2) source: 3 weeks-seedlings treated with 250 mM NaCl for 5hours


title: 1000_5_C0301_T0301

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone trans-Zeatin and cultured for 3 d. The concentration of the plant hormone was adjusted to 1microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, trans-Zeatin, Callus

source_name: Target (CH2) source: Callus treated with 1 microM trans-Zeatin for 3 days


title: 2107_1_C0101_T0101

description:
Control (CH1): Leaves at stage of 4th-leaf completely expanded of the japonica rice variety Taichung 65 were grown in modified white's medium at 18 degrees C. Then RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves at stage of 4th-leaf completely expanded of strong virlecent mutant "yl-stb" from the japonica rice variety Taichung 65 were grown in modified white's medium at 18 degrees C. Then RNA was labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Virlecent ,

source_name: Control (CH1) source: Leaves at stage of 4th-leaf completely expanded of wild type grown in 18 degreesC

source_name: Target (CH2) source: Leaves at stage of 4th-leaf completely expanded of strong virlecent mutant


title: 1000_3_C0401_T0401

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone Brassinosteroid and cultured for 3 d. The concentration of the plant hormone was adjusted to 0.02 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Brassinosteroid, Callus

source_name: Control (CH1) source: Non treated callus (grown on MS medium including 2.4D for 30 days)

source_name: Target (CH2) source: Callus treated with  0.02 microM Brassinosteroid for 3 days


title: 2105_2_C0301_T0304

description:
Control (CH1): 18-day-old seedlings (except root) of the japonica rice variety Nipponbare was cultuered in water using Hyponex 10-3-3 (1/1000 dilution) at 28 degrees C (16 hours light, 8 hours dark), and then harvested at 4 days after  gamma-ray unirradiation (0min)  (= after same actions without gamma-ray irradiation). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Target (CH2): 18-day-old seedlings (except root) of the japonica rice variety Nipponbare was cultuered in water using Hyponex 10-3-3 (1/1000 dilution) at 28 degrees C (16 hours light, 8 hours dark), and then harvested at 4 days after  gamma-ray unirradiation (78.2Gy = 9.2Gy/min x 8.5min). After harvesting, we used an RNeasy Plant Mini Kit (QIAGEN) to extract total RNA from the plants. Total RNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, Gamma-ray,

source_name: Control (CH1) source: Seedling of 4days after gamma-ray unirradiation (actions without gamma-ray irradiation)

source_name: Target (CH2) source: 18day-old seedlings (except root) after 4days of gamma irradiation


title: 1000_3_C0301_T0301

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone Brassinosteroid and cultured for 3 d. The concentration of the plant hormone was adjusted to 0.05 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Brassinosteroid, Callus

source_name: Target (CH2) source: Callus treated with  0.05 microM Brassinosteroid for 3 days


title: 1000_21_C0001_T0001

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 30 min. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA, Callus

source_name: Target (CH2) source: Callus treated with 50 microM ABA for 30 min


title: 2102_2_C0001_T0001

description:
Control (CH1): The japonica rice variety Nipponbare were grown hydrponically for 7-days without treatment. Leaves of plants used for total RNA extraction by phenol-SDS method. Messenger RNA was purified by oligo(dT) cellulose, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown hydrponically for7-days that treated with 50 mM NaCl for 1 hour. Leaves of plants used for total RNA extraction by phenol-SDS method. Messenger RNA was purified by oligo(dT) cellulose, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Salt, ,

source_name: Control (CH1) source: Seedling (leaf) grown hydrponically for 7 days without treatment

source_name: Target (CH2) source: 7 days-grown leaves by the hydoroponics treated with 50 mM NaCl for 1 hour


title: 2103_2_C0001_T0001

description:
Control (CH1): The japonica rice variety Pokkali were grown hydroroponically at 3-4 leaf stage without salt treatment. 3th-5th leaves of the plants used for total RNA extraction by CTAB method. Messenger RNA was purified by magnet purified kit (CPG), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Pokkali were grown in diluted sea water (50mM NaCl) for 24 days after grown hydroponically at 3-4 leaf stage. 3th-5th leaves of the plants used for total RNA extraction by CTAB method. Messenger RNA was purified by magnet purified kit (CPG), labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Salt, ,

source_name: Control (CH1) source: Leaf (3-4 leaf stage) of Pokkali, non-treatment

source_name: Target (CH2) source: 24 days-grown leaves after the treatment with diluted  sea water (50mM NaCl)


title: 1000_6_C0001_T0001

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone Jasmonic acid and cultured for 3 d. The concentration of the plant hormone was adjusted to 100microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, Jasmonic acid, Callus

source_name: Target (CH2) source: Callus treated with 100microM Jasmonic acid for 3 days


title: THP-1 A12 mutant cells, PMA stimulation, oxLDL loading, 5 days

status: Public on Aug 11 2009

city: Utrecht

first: Joost

middle: Ougust

last: Fledderus

address: Heidelberglaan 100, Huispostnummer G02-402

department: Vascular Medicine

country: Netherlands

institute: University Medical Center Utrecht

hyb_protocol: Each cRNA sample (1 micrograms; Cy5-labeled) was hybridized in duplicate against a common reference cRNA sample (1 micrograms; Cy3-labeled), for 16 hours at 40 degrees Celsius.

scan_protocol: Agilent scanner: resolution: 10 micrometer, scan area: 60 x 21.6 mm, PMT: 50%, Laser power: 50%

data_processing: After print-tip Loess-normalization (Loess span: 0.3; limma package, Bioconductor, available online: http://www.bioconductor.org), and background subtraction, the microarray intensity data imported in the Rosetta Resolver database.

organism: Homo sapiens

source_name: common reference pool

label_protocol: Within these cRNAs the molar ratio of incorporated aminoallyl-rUTP (A5660, Sigma, St. Louis, MO) to rUTP was 1:1. Cy5 mono reactive dyes (PA25001, Amersham Biosciences, Piscataway, NJ) were coupled according to the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy purification kit (Qiagen GmbH, Hilden, Germany).

growth_protocol: Cells were maintained in RPMI/FBS, 100U/ml penicillin and 100mg/ml streptomycin, plated at a density of 1x106 cells per ml and pretreated for 24 hours with 100nM of phorbol myristate acetate (PMA) (Sigma, St. Louis, MO) to induce differentiation into adherent macrophages. Subsequently, cells were washed with RPMI 1640 medium to remove PMA.

extract_protocol: Total RNA molecules were isolated from HUVEC by Trizol, and treated with DNAse-I, and then purified by using RNeasy spin columns (Qiagen). Thereafter, mRNA of each component was linearly amplified for one round (MessageAmp aRNA kit, #1750, Ambion), synthesizing antisense cRNAs.

treatment_protocol: To induce foam cell formation, 100 mg/ml ox-LDL in RPMI/FBS was added and culturing was continued for 0, 5 or 8 days with intermediate refreshing of medium every 3 days.

tag: Human acute monocytic leukemia cell line


title: THP-1 A3 mutant cells, PMA stimulation, oxLDL loading, 5 days


title: 1000_2_C0301_T0301

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 10 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA, Callus

source_name: Target (CH2) source: Callus treated with 10 microM ABA for 3 days


title: 1000_7_C0201_T0201

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone Cyclooctane and cultured for 3 d. The inhibitor of plant hormone (Ethylene) synthesis was added 15 microL to MS medium . After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Ethylene, Cyclooctane, Callus

source_name: Target (CH2) source: Callus treated with 15 microL Cyclooctane for 3 days


title: THP-1 A12 mutant cells, unstimulated

source_name: THP-1 A12 mutant cells, unstimulated


title: THP-1 A12 mutant cells, PMA stimulation, 8 days


title: THP-1 A3 mutant cells, unstimulated

source_name: THP-1 A3 mutant cells, unstimulated


title: 1000_1_C0301_T0301

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA and cultured for 3 d. The concentration of the plant hormone was adjusted to 10 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA, Callus

source_name: Target (CH2) source: Callus treated with 10 microM GA3 for 3 days


title: 1000_2_C0201_T0201

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone ABA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, ABA, Callus

source_name: Control (CH1) source: Non treated callus (grown on MS medium including 2.4D for 30 days)

source_name: Target (CH2) source: Callus treated with 50 microM ABA for 3 days


title: 1000_1_C0201_T0201

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA, Callus

source_name: Target (CH2) source: Callus treated with 50 microM GA3 for 3 days


title: THP-1 cells, PMA stimulation, oxLDL loading, 5 days


title: 1000_22_C0001_T0001

description:
Control (CH1): The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA and cultured for 30 min. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was labeled, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of mRNA from hormone-treated callus by the signal intensity of that from untreated callus according the protocol of above reference. *Murashige, T. andSkoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473-497.
Target (CH2):
Keyword: Rice microarray project, Rice 8987 EST array, Hormonal, GA, Callus

source_name: Target (CH2) source: Callus treated with 50 microM GA3 for 30 min


title: THP-1 A3 mutant cells, PMA stimulation, oxLDL loading, 8 days


title: THP-1 cells, unstimulated

source_name: THP-1 cells, unstimulated


title: 2101_2_C0001_T0005

description:
Control (CH1): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with H2O for 5 hours as control plant. Whole plants used for RNA extraction. Messenger RNA was labeled purified by Oligo(dT)-latex, by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with low temperature (4 degrees C) for 5hours as target plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: 3 weeks seedlings (whole plant) treated with H2O for 5 hours

source_name: Target (CH2) source: 3 weeks-seedlings treated with 4 degrees C for 5hours


title: 2101_2_C0001_T0003

description:
Control (CH1): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with H2O for 5 hours as control plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The japonica rice variety Nipponbare were grown for 3 weeks at 28 degrees C under dark condition. The plants were treated with dehydration condition for 5hours as target plant. Whole plants used for RNA extraction. Messenger RNA was purified by Oligo(dT)-latex, labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Drought, ,

source_name: Target (CH2) source: 3 weeks-whole plants grown under dark condition with dehydration treatment  for 5 hours


title: THP-1 A12 mutant cells, PMA stimulation, oxLDL loading, 8 days


title: THP-1 A12 mutant cells, PMA stimulation, 5 days


title: THP-1 A3 mutant cells, PMA stimulation, 8 days


title: THP-1 A3 mutant cells, PMA stimulation, 5 days


title: THP-1 cells, PMA stimulation, 5 days

source_name: THP-1 cells, PMA stimulation, 5 days


title: THP-1 cells, PMA stimulation, oxLDL loading, 8 days


title: THP-1 cells, PMA stimulation, 8 days

source_name: THP-1 cells, PMA stimulation, 8 days


title: Wild type1

city: Shanghai

first: Xiangyin

last: kong

address: No.225 yueyang road

department: molecular genetics

country: China

institute: Institute of health science

description: Wild type

hyb_protocol: Euk 20X must be heated 5 minutes before using it. Vortex before using and spin down. Put on ice when you’re finished with it but not before adding it to MasterMix. (multiply all by 3.5) MasterMix components 2X Hybe Buffer 150.0 µL 525.0 µL DEPC H20 54.0 µL (to bring volume up to 300.0µL) 189.0 µL 100% DMSO 30.0 µL 105.0 µL Eukaryotic 20X Control *** 15.0 µL 52.5 µL Oligo B2 5.0 µL 17.5 µL Herring Sperm DNA 3.0 µL 10.5 µL BSA 3.0 µL 10.5 µL cRNAfragmented 40.0 µL (if you retrieve all from NanoDrop) you have these separate 1. Keep cRNA in tubes labeled FRAG. 2. Prepare MasterMix in 15mL corning tube. 3. Mix after each component by pipetting several times. 4. Add 260.0 µL of the Hybe MasterMix to each fragmented sample. You total volume should be 300.0 µL. 5. If you are not hybridizing right away, store the cRNA-HybeCocktail mix in the -20°C until you’re ready to use it. HYBRIDIZATION Thaw Hybe Cocktails if they are frozen before heating. Pull arrays out of 4°C Deli Fridge 30 minutes before you want to load them. They must be at room temperature before you pierce the septa to prevent leakage. 1. Put tube hats on to prevent popping open at high heat. 2. Place the tubes into the 95°C heating block for 5 minutes. 3. Move the tubes to the 45°C heating block, again for 5 minutes. 4. Spin in MicroFuge at max. speed for 5 minutes. 5. Load 250.0 µL into each array. 6. Put in Hybe Oven, set at 60rpm and 45°C for 16 hours. After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of Non-Stringent Wash Buffer (Wash Buffer A) Wash Buffer A: Non-Stringent Wash Buffer (6X SSPE, 0.01% Tween-20) For 1,000 mL: 300 mL of 20X SSPE 1.0 mL of 10% Tween-20 699 mL of water Filter through a 0.2 μm filter EukGE-WS2v5* Midi_euk2* 10 cycles of 2 mixes/cycle with Wash Buffer A at 30°C 6 cycles of 15 mixes/cycle with Wash Buffer B at 50°C Stain the probe array for 5 minutes in SAPE solution at 35°C 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C Stain the probe array for 5 minutes in antibody solution at 35°C Stain the probe array for 5 minutes in SAPE solution at 35°C 15 cycles of 4 mixes/cycle with Wash Buffer A at 35°C. The holding temperature is 25°C

scan_protocol: [Scanner] Pixel Size 1.56 hardware: GeneChip Scanner 3000 Affymetrix® Microarray Suite Filter 570 Scanner ID 50101490 Number of Scans 1 Scanner Type M10 As affymetrix protocol.

data_processing: Data in value is raw data (Mas5 scaled) unaltered by normalizations.

label: Biotin

organism: Mus musculus

source_name: Postnatal Day 0.5 lens tissue, wildtype

label_protocol:
Test RNA sample on NanoDrop. Concentration must be 500_g/µL or more. Calculate the volume of RNA sample necessary to start protocol with 5µg. i.e. (5 µg) / (NanoDrop concentration reading in µg/µL) = µL
RNA x uL
DEPC H20 10-x uL
oligo T7 2.0 µL
1. Add all components together in a 0.2µL strip tube.
2. Mix well and spin down.
3. Place in thermalcycler at 70°C for 10 minutes. Should be warming up to 70°C while you prep. the samples.
4. Allow thermalcycler to ramp down to 4°C.
5. 4°C for 2 minutes. Spin down and put on ice.
6. Prepare the 1st Strand MasterMix.
Reverse Transcription (RT) 1st Strand
You should have thawed and vortexed the components during the 70°C-10 minute step.
5X 1st Strand Mix (4.0 µL) /sample
0.1M DTT (2.0 µL) /sample
10mM dNTPs (1.0 µL) /sample
7.0 µL total
1. Add 7.0 µL 1st Strand MasterMix to each sample. Mix.
2. Put on thermalcycler 42°C-1 Hour. Set timer for 2 minutes.
(This setting is actually programmed for 42°C for 1 hour and 3 minutes, to compensate for the extra 2
minutes at the beginning before adding the SuperScript II.
3. After 2 minutes at 42°C add 1.0 µL of SSII enzyme. (Addition should be done on thermalcycler)
4. The rest of the program will run, 1 hour at 42°C.
5. Proceed to 2nd Strand.
(components should be thawed ~10 minutes before thermalcycler finishes.)
Reverse Transcription (RT) 2nd Strand
DEPC H20 91.0 µL /sample
5X 2nd Strand Mix 30.0 µL /sample
E. coli DNA Polymerase I (DNA Pol I) 4.0 µL /sample
10mM dNTPs 3.0 µL /sample
E. coli DNA ligase (ligase) 1.0 µL /sample
RNase H 1.0 µL /sample
1. Put samples on thermalcycler, 16°C for 2 hours.
2. At 2 hours, add 2.0 µL of T4 DNA Polymerase. Mix.
3. Run additional 5 minutes at 16°C.
4. Transfer samples to 1.5mL tube with 10.0 µL of 0.5M EDTA. Vortex.
5. Use cDNA Clean-Up Module to clean up samples.
Clean-Up of Double Stranded cDNA
Necessary components:
1.5mL tube with cDNA and EDTA, mixed.
cDNA Binding Buffer
cDNA Wash Buffer (ethanol added by MCF)
cDNA Elution Buffer
cDNA clean-up column (in 4°C Deli Fridge)
Empty Collection Tube (provided in clean-up module)
Empty 1.5mL tube labeled with sample name for collecting final eluate.
MicroFuge 18 Centrifuge to spin down samples.
cDNA Wash Buffer is supplied as a concentrate and you have to add ethanol before using. Check the tube before use to make sure that etOH has been added.
1. Label Collection Tube with sample name (on side).
2. Add 600.0 µL of cDNA Binding Buffer (yellow) into tube with sample and EDTA.
3. Vortex. Spin down briefly (2 sec.)
4. Add 500.0 µL sample-Binding Buffer mix onto column.
5. Spin in MicroFuge 18 Centrifuge, 14,000rpm for 1 minute.
6. Pour eluate down sink. Keep same collection tube.
7. Add the remaining cDNA-Binding Buffer mix onto column.
8. Spin 14K rpm for 1 minute.
9. Discard that collection tube and place column into new, labeled tube.
10. Add 720.0 µL cDNA Wash Buffer (ETOH added) to the column.
11. Spin 14K rpm for 1 minute.
12. Discard eluate into sink. Replace column into collection tube.
13. Spin empty column with the lid open for 5 minutes at 14K rpm.
14. Place column into labeled 1.5mL tube. Discard collection tube.
15. Air dry column for an additional minute (cover with KimWipe).
16. Add 14.0 µL Elution Buffer onto the center of the column.
17. Let sit at room temp for 1 minute.
18. Spin at 14K for 1 minute.
19. Discard column.
20. Measure the eluate volume.
21. Bring volume up to 20.0 µL with DEPC H20.
22. Store at -20ºC until ready to proceed with IVT step.
InVitro Transcription Reaction (IVT): production of biotin-labeled cRNA
cDNA should be at 20.0 µL before adding IVT MasterMix components.
IVT kit components should be thawed to room temp. ~20 minutes before using.
10X IVT Labeling Buffer (may have precipitate, mix well.) (4.0 µL) /sample
IVT Labeling NTP Mix (12.0 µL) /sample
IVT Labeling Enzyme Mix (4.0 µL) /sample
1. Mix components. Spin briefly.
2. Add 20.0 µL IVT MasterMix to each sample. Mix by pipetting.
3. 37 ºC for 16 hours in thermalcycler.
4. Clean-up cRNA with cRNA Clean-Up Module.
Clean-Up of Biotinylated cRNA with cRNA Clean-Up Module
Necessary Components:
cRNA Binding Buffer
cRNA Wash Buffer (ethanol added by MCF)
cRNA clean-up column (stored at 4°C in deli fridge)
Collection Tube (labeled with sample name on side)
DEPC H20
100% Ethanol
80% Ethanol
2 clean, labeled 1.5mL tubes
1. Transfer cRNA samples into clean, labeled 1.5mL tubes for clean-up.
2. Add 60.0 µL to each sample. Vortex to mix and spin down.
3. Add 350.0 µL cRNA Binding Buffer to each sample. Vortex and spin down.
4. Add 250.0 µL 100% ETOH to each sample. Mix by pipetting.
5. Add cRNA-Binding Buffer-ETOH mix onto column (it all fits).
6. Spin at 14,000rpm on “Short Spin” setting (30 seconds).
7. Place columns into clean, labeled collection tube. Discard previous tubes with eluate.
8. Add 500.0 µL cRNA Wash Buffer to each column.
9. Spin at 14K for “Short Spin”.
10. Discard eluate in sink but replace column into collection tube.
11. Add 500.0 µL 80% ETOH onto column.
12. “Short Spin” at 14K.
13. Discard eluate and replace columns into collection tube again.
14. Spin 14K for 5 minutes to dry column.
15. Put column into clean, labeled 1.5mL tube. (This tube should have the request number, the term “IVT” and the sample name on top. On the side put the PI last name and the date.)
16. Pipet 11.0 µL DEPC H20 onto center of column.
17. Spin 14K for 1 minute.
18. Add another 10.0 µL DEPC H20 onto center of column.
19. Spin 14K for 1 minute.
20. Measure volume of eluate. Record the volume in your lab notebook.
21. NanoDrop samples. Dilute with DEPC H20 if you need to, to get concentration into read-able range for NanoDrop (under 3000_g).
22. Make a dilution of the IVT samples for testing on the Agilent.
Perform calculations to determine adjusted cRNA amount. Enter the total µg into MAID. Perform calculations for Fragmentation step and record the volumes in your lab notebook. Calculations are done with the IVT NanoDrop adjusted cRNA concentrations acquired with the formula provided by Affy.
Fragmentation:
cRNA (X uL) 15ug
DEPC H20(variable) (32-x) µL
5X Fragmentation Buffer 8.0 µL
40.0 uL
1. Add 8.0 µL 5X Frag. Buffer to each empty 1.5mL tube.
2. Add the required amount of water to each tube. This amount will depend on the concentration of cRNA- how much cRNA to make 15 µg of fragmented cRNA, then how much DEPC H20 to bring the final volume to 40.0 µL?
3. Add the required amount of cRNA to each tube.
4. Make sure the 1.5mL tube is clearly labeled FRAG so that you can tell it apart from the IVT cRNA tube.
5. Put the FRAG tube onto the 99°C heat block for 35 minutes.
6. After fragmentation put the tube on ice. Let it cool about 5 minutes on ice.
7. Spin in the MicroFuge at max. speed to get the condensation out of the lid.
8. Vortex and spin.
9. Test FRAG on NanoDrop. Needs to be 15 µg or more. (15 µg/40 µL=0.375 µg/µL or more)
Put the FRAG into hybridization cocktail and store at -20°C until you are ready to load it onto a chip.

extract_protocol: RNA was isolated using Qiagen RNeasy mini kits. On column DNase digestion was used. RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Affymatrix Bioanalyzer system.

treatment_protocol: Lens were dissected from day 0.5 animals and placed in RNAlater (Ambion) for 24 hours at 4 degrees Celsius. After 24 hours, the RNAlater was removed and the lens were frozen on dry ice and placed in a -80 degree freezer.

tag: Background Srain

tag: Gender

value: Male

tag: Tissue

value: lens

tag: Age

value: 0.5 Days Postnatal


title: HSF4 knockout2

description: sxh ko2

data_processing: Data in value is raw data (Mas5 scaled) unaltered by normalizations

source_name: Postnatal Day 0.5 lens tissue, HSF4 knockout


title: Pool Normal chow-2 days AJ mouse strain versus Pool Normal chow-2 days B6 mouse strain replicate 3

status: Public on Aug 09 2009

city: Lausanne

first: Carine

last: Poussin

address: Quartier UNIL-Sorge

country: Switzerland

institute: University of Lausanne

description: Replicate 3 of 3 for pool 2d NC AJ mice / pool 2d NC B6 mice

hyb_protocol: Cy5-labeled RNA from individual liver sample and Cy3-labeled pool of RNA from 6 liver samples were hybridized on the M17K spotted array according published protocols (de Fourmestraux, J Biol Chem, 2004)

scan_protocol: Scanned on a Scanarray 4000 scanner. For each slide, 2 scans were performed to obtain signals with higher and lower (Low) intensities. Combining high and low scans using a mathematical method published in BMC Genomics (Ref: Lyng H et al, BMC Genomics, 5(1):10, 2004) allowed to increase the dynamic range of signal intensities and to prevent from having saturated signal intensities. For few slides, only 1 scan could be performed (in that case, informations contained in txt files are the same for high and low scans). Tiff image analysis was done using the software ImaGene 4 (from BioDiscovery) in order to extract spot intensity signal for Cy3 and Cy5 channels.

data_processing: Print Tip Lowess normalized data obtained from log2 of processed Red signal/processed Green signal. The sma (Statistical Microarray Analysis) package from the statistical R software was used.

source_name: Pool of amplified total RNA from liver of 6 normal chow fed (for 2 days)-AJ mice

label_protocol: Indirect labeling of amplified RNA with Cy3 or Cy5 fluorescent dye according to published protocols (de Fourmestraux, J Biol Chem, 2004)

growth_protocol: Five/six-week-old C57BL/6J male mice (Janvier, France) and A/J (Jackson laboratory via Charles River, Germany) were fed a normal chow (NC; 12% fat, 60% carbohydrates and 28% proteins) or a high fat diet (HFD; 58% fat, 26% carbohydrates, 16% proteins) for 2, 10 or 30 days. At each time point, mice were killed in the fed state after isofluran anesthesia. Liver samples were rapidly dissected, snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol: RNA from each frozen liver sample was extracted as described in the protocol of peqGOLD TriFast (from peqLab). RNA quality was checked before and after amplification with a bioanalyzer 2100 (Agilent). RNA was reverse transcribed and RNA was amplified with MessageAmpTM kit (Ambion) according the manufacturer'sprotocol.

tag: A/J mouse

source_name: Pool of amplified total RNA from liver of 6 normal chow fed (for 2 days)-B6 mice

tag: C57BL/6J mouse


title: Pool Normal chow-2 days B6 mouse strain versus Pool Normal chow-2 days AJ mouse strain replicate 2

description: Replicate 2 of 3 for pool 2d NC B6 mice / pool 2d NC AJ mice


title: IS 2

status: Public on Aug 10 2009

city: La Jolla

first: Hang

last: Yao

state: CA

address: 9500 Gilman Dr

country: USA

institute: UCSD

description: This sample was made from cultured hippocampal slices treated with IS for 2 hours.

hyb_protocol: Hybridizations were carried out by using the Illumina gene expression system according to the manufacturer's instructions.

scan_protocol: Illumina scanner

data_processing: Raw data were aquired using BeadStudio 2.0. The background were subtracted and normalised.

source_name: Hippocampus

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit following the manufacturer's instructions. Input amount: 100ng of total RNA.

extract_protocol: Total RNA was extracted from cultured hippocampal slices using RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: Strain

value: Mixed gender

value: Organotypic hippocampal slice culture


title: Control ACSF 2

description: This sample is a control for IS-treated slices.

value: Mixed

value: Organotypic hippocampal slice cultures


title: ACSF + DIDS 3

description: This sample was made from cultured mouse hippocampal slices incubated with ACSF+DIDS for 2 hours.


title: IS + DIDS 3

description: This sample was made from cultured mouse hippocampal slices treated with IS+DIDS for 2 hours.


title: Pool Normal chow-2 days B6 mouse strain versus Pool Normal chow-2 days AJ mouse strain replicate 3

description: Replicate 3 of 3 for pool 2d NC B6 mice / pool 2d NC AJ mice


title: HSF4 knockout1

description: HSF4 knockout


title: ACSF + DIDS 1

description: This sample was make from cultured mouse hippocampal slices treated with ACSF+DIDS for 2 hours.


title: High Fat Diet-30 days replicate 5 B6 mouse strain

description: Biological replicate 5 of 6 for 30d HFD / pool 30d NC (B6 mice)

source_name: Amplified total RNA from liver of high fat fed (for 30 days)-mouse

source_name: Pool of amplified total RNA from liver of 6 normal chow fed (for 30 days)-mice


title: IS + DIDS 1


title: IS 3

description: This sample was made from cultured mouse hippocampal slices incubated with IS for 2 hours.


title: IS + DIDS 2


title: Wild type2

description: Wild type2


title: Control ACSF 3

description: This sample was made from cultured mouse hippocampal slices incubated with ACSF for 2 hours.


title: ACSF + DIDS 2

description: This sample was made from cultured mouse hippocampal slices itreated with IS+DIDS for 2 hours.


title: Pool Normal chow-2 days AJ mouse strain versus Pool Normal chow-2 days B6 mouse strain replicate 1

description: Replicate 1 of 3 for pool 2d NC AJ mice / pool 2d NC B6 mice


title: Pool Normal chow-2 days AJ mouse strain versus Pool Normal chow-2 days B6 mouse strain replicate 2

description: Replicate 2 of 3 for pool 2d NC AJ mice / pool 2d NC B6 mice


title: Pool Normal chow-2 days B6 mouse strain versus Pool Normal chow-2 days AJ mouse strain replicate 1

description: Replicate 1 of 3 for pool 2d NC B6 mice / pool 2d NC AJ mice


title: High Fat Diet-10 days replicate 1 B6 mouse strain

description: Biological replicate 1 of 6 for 10d HFD / pool 10d NC (B6 mice)

source_name: Amplified total RNA from liver of high fat fed (for 10 days)-mouse

source_name: Pool of amplified total RNA from liver of 6 normal chow fed (for 10 days)-mice


title: High Fat Diet-2 days replicate 2 B6 mouse strain

description: Biological replicate 2 of 6 for 2d HFD / pool 2d NC (B6 mice)

source_name: Amplified total RNA from liver of high fat fed (for 2 days)-mouse

source_name: Pool of amplified total RNA from liver of 6 normal chow fed (for 2 days)-mice


title: High Fat Diet-30 days replicate 3 B6 mouse strain

description: Biological replicate 3 of 6 for 30d HFD / pool 30d NC (B6 mice)


title: High Fat Diet-2 days replicate 6 B6 mouse strain

description: Biological replicate 6 of 6 for 2d HFD / pool 2d NC (B6 mice)


title: Control ACSF 1

extract_protocol: Total RNA was extracted from cultured slices using RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.


title: IS 1

description: This sample was made from cultured hippocampal slices treated with IS for 2 hours.

label: Label Biotin

extract_protocol: Total RNA was extracted from organotypic hippocampal slice cultures using RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.


title: High Fat Diet-30 days replicate 6 B6 mouse strain

description: Biological replicate 6 of 6 for 30d HFD / pool 30d NC (B6 mice)


title: High Fat Diet-2 days replicate 3 B6 mouse strain

description: Biological replicate 3 of 6 for 2d HFD / pool 2d NC (B6 mice)


title: High Fat Diet-10 days replicate 6 B6 mouse strain

description: Biological replicate 6 of 6 for 10d HFD / pool 10d NC (B6 mice)


title: High Fat Diet-30 days replicate 1 B6 mouse strain

description: Biological replicate 1 of 6 for 30d HFD / pool 30d NC (B6 mice)


title: High Fat Diet-10 days replicate 5 B6 mouse strain

description: Biological replicate 5 of 6 for 10d HFD / pool 10d NC (B6 mice)


title: Normal chow-2 days replicate 6 B6 mouse strain

description: Biological replicate 6 of 6 for 2d NC / pool 2d NC (B6 mice)

source_name: Amplified total RNA from liver of normal chow fed (for 2 days)-mouse


title: High Fat Diet-2 days replicate 4 B6 mouse strain

description: Biological replicate 4 of 6 for 2d HFD / pool 2d NC (B6 mice)


title: Normal chow-2 days replicate 4 B6 mouse strain

description: Biological replicate 4 of 6 for 2d NC / pool 2d NC (B6 mice)


title: High Fat Diet-30 days replicate 4 B6 mouse strain

description: Biological replicate 4 of 6 for 30d HFD / pool 30d NC (B6 mice)


title: High Fat Diet-10 days replicate 2 B6 mouse strain

description: Biological replicate 2 of 6 for 10d HFD / pool 10d NC (B6 mice)


title: High Fat Diet-30 days replicate 2 B6 mouse strain

description: Biological replicate 2 of 6 for 30d HFD / pool 30d NC (B6 mice)


title: High Fat Diet-10 days replicate 3 B6 mouse strain

description: Biological replicate 3 of 6 for 10d HFD / pool 10d NC (B6 mice)


title: High Fat Diet-10 days replicate 4 B6 mouse strain

description: Biological replicate 4 of 6 for 10d HFD / pool 10d NC (B6 mice)


title: High Fat Diet-2 days replicate 5 B6 mouse strain

description: Biological replicate 5 of 6 for 2d HFD / pool 2d NC (B6 mice)


title: High Fat Diet-30 days replicate 1 AJ mouse strain

description: Biological replicate 1 of 6 for 30d HFD / pool 30d NC (A/J mice)


title: Normal chow-2 days replicate 5 B6 mouse strain

description: Biological replicate 5 of 6 for 2d NC / pool 2d NC (B6 mice)


title: High Fat Diet-2 days replicate 1 B6 mouse strain

description: Biological replicate 1 of 6 for 2d HFD / pool 2d NC (B6 mice)


title: High Fat Diet-30 days replicate 3 AJ mouse strain

description: Biological replicate 3 of 6 for 30d HFD / pool 30d NC (A/J mice)


title: Normal chow-2 days replicate 3 B6 mouse strain

description: Biological replicate 3 of 6 for 2d NC / pool 2d NC (B6 mice)


title: Normal chow-2 days replicate 1 B6 mouse strain

description: Biological replicate 1 of 6 for 2d NC / pool 2d NC (B6 mice)


title: High Fat Diet-10 days replicate 5 AJ mouse strain

description: Biological replicate 5 of 6 for 10d HFD / pool 10d NC (A/J mice)


title: High Fat Diet-30 days replicate 6 AJ mouse strain

description: Biological replicate 6 of 6 for 30d HFD / pool 30d NC (A/J mice)


title: High Fat Diet-30 days replicate 5 AJ mouse strain

description: Biological replicate 5 of 6 for 30d HFD / pool 30d NC (A/J mice)


title: High Fat Diet-30 days replicate 4 AJ mouse strain

description: Biological replicate 4 of 6 for 30d HFD / pool 30d NC (A/J mice)


title: High Fat Diet-10 days replicate 6 AJ mouse strain

description: Biological replicate 6 of 6 for 10d HFD / pool 10d NC (A/J mice)


title: High Fat Diet-30 days replicate 2 AJ mouse strain

description: Biological replicate 2 of 6 for 30d HFD / pool 30d NC (A/J mice)


title: High Fat Diet-10 days replicate 2 AJ mouse strain

description: Biological replicate 2 of 6 for 10d HFD / pool 10d NC (A/J mice)


title: High Fat Diet-10 days replicate 4 AJ mouse strain

description: Biological replicate 4 of 6 for 10d HFD / pool 10d NC (A/J mice)


title: High Fat Diet-10 days replicate 3 AJ mouse strain

description: Biological replicate 3 of 6 for 10d HFD / pool 10d NC (A/J mice)


title: Normal chow-2 days replicate 3 AJ mouse strain

description: Biological replicate 3 of 6 for 2d NC / pool 2d NC (A/J mice)


title: Normal chow-2 days replicate 1 AJ mouse strain

description: Biological replicate 1 of 6 for 2d NC / pool 2d NC (A/J mice)


title: High Fat Diet-2 days replicate 6 AJ mouse strain

description: Biological replicate 6 of 6 for 2d HFD / pool 2d NC (A/J mice)


title: High Fat Diet-2 days replicate 1 AJ mouse strain

description: Biological replicate 1 of 6 for 2d HFD / pool 2d NC (A/J mice)


title: Normal chow-2 days replicate 2 AJ mouse strain

description: Biological replicate 2 of 6 for 2d NC / pool 2d NC (A/J mice)


title: Normal chow-2 days replicate 5 AJ mouse strain

description: Biological replicate 5 of 6 for 2d NC / pool 2d NC (A/J mice)


title: High Fat Diet-2 days replicate 2 AJ mouse strain

description: Biological replicate 2 of 6 for 2d HFD / pool 2d NC (A/J mice)


title: Normal chow-2 days replicate 4 AJ mouse strain

description: Biological replicate 4 of 6 for 2d NC / pool 2d NC (A/J mice)


title: Normal chow-2 days replicate 6 AJ mouse strain

description: Biological replicate 6 of 6 for 2d NC / pool 2d NC (A/J mice)


title: High Fat Diet-2 days replicate 3 AJ mouse strain

description: Biological replicate 3 of 6 for 2d HFD / pool 2d NC (A/J mice)


title: High Fat Diet-2 days replicate 5 AJ mouse strain

description: Biological replicate 5 of 6 for 2d HFD / pool 2d NC (A/J mice)


title: High Fat Diet-10 days replicate 1 AJ mouse strain

description: Biological replicate 1 of 6 for 10d HFD / pool 10d NC (A/J mice)


title: Desulfovibrio Acetone Stress Slide Z

status: Public on Aug 08 2009

city: Knoxville

first: Qiang

last: He

state: TN

address: 57A Perkins Hall

department: Civil and Environmental Engineering

institute: The University of Tennessee

description: The objective of this study is to investigate the stress response of the sulfate-reducing bacterium Desulfovibrio vulgaris to elevated concentrations of acetone as a solvent, which is a common co-contaminant in subsurface environments.

data_processing: Lowess intensity-based normalization. He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subjected to acetone stress

treatment_protocol: Culture was treated by 5% (v/v) acetone for 100 minutes

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase in standard Lactate-Sulfate medium followed by exposure to acetone as a stressor.

source_name: Desulfovibrio vulgaris control culture

treatment_protocol: Control culture without treatment

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase in standard Lactate-Sulfate medium without exposure to acetone as a stressor.


title: Desulfovibrio Acetone Stress Slide T

hyb_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Desulfovibrio Acetone Stress Slide U

scan_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Desulfovibrio Acetone Stress Slide V

label_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: High Fat Diet-2 days replicate 4 AJ mouse strain

description: Biological replicate 4 of 6 for 2d HFD / pool 2d NC (A/J mice)


title: Desulfovibrio Acetone Stress Slide Q

growth_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Desulfovibrio Acetone Stress Slide Y

extract_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Desulfovibrio Acetone Stress Slide S


title: Desulfovibrio Acetone Stress Slide R


title: Desulfovibrio Acetone Stress Slide M

treatment_protocol: Culture was treated by 5% (v/v) acetone for 30 minutes


title: Desulfovibrio Acetone Stress Slide H


title: Desulfovibrio Acetone Stress Slide G


title: Desulfovibrio Acetone Stress Slide C


title: Desulfovibrio Acetone Stress Slide D


title: Desulfovibrio Acetone Stress Slide B


title: Desulfovibrio EtOH Stress Slide W

description: The objective of this study is to investigate the stress response of the sulfate-reducing bacterium Desulfovibrio vulgaris to elevated concentrations of ethanol as a solvent, which is a common co-contaminant in subsurface environments.

hyb_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.  PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

source_name: Desulfovibrio vulgaris subjected to ethanol stress

treatment_protocol: Culture was treated by 5% (v/v) for 100 minutes

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase in standard Lactate-Sulfate medium followed by exposure to ethanol as a stressor.

tag: Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase in standard Lactate-Sulfate medium without exposure to ethanol as a stressor.


title: Desulfovibrio Acetone Stress Slide A


title: Desulfovibrio EtOH Stress Slide K

scan_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.  PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

treatment_protocol: Culture was treated by 5% (v/v) for 30 minutes


title: Desulfovibrio EtOH Stress Slide 1

label_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.  PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553

treatment_protocol: Culture was treated by 5% (v/v) for 100 minutes.


title: Desulfovibrio Acetone Stress Slide 2


title: Desulfovibrio EtOH Stress Slide I

growth_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.  PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Desulfovibrio EtOH Stress Slide E

extract_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381.  PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553


title: Desulfovibrio EtOH Stress Slide J


title: Desulfovibrio EtOH Stress Slide 7


title: Desulfovibrio EtOH Stress Slide L


title: Desulfovibrio EtOH Stress Slide 3


title: Desulfovibrio EtOH Stress Slide N


title: Desulfovibrio EtOH Stress Slide F


title: Normal chow-2 days replicate 2 B6 mouse strain

description: Biological replicate 2 of 6 for 2d NC / pool 2d NC (B6 mice)


title: CAT at 24h, biological replicate 3

status: Public on Aug 06 2009

city: Munich

first: Lothar

middle: J.

last: Strobl

address: Marchioninistr. 25

department: Department of Gene Vectors

country: Germany

institute: Helmholtz Zentrum München, German Research Center for Environmental Health

description: gene expression data from cells with 24h CAT expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU 133 PLUS 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: CAT expression 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Cells were estrogen depleted for 3 days and Notch1-IC, Notch2-IC, CAT and EBNA2 were induced for different time periods (0h, 4h, 8h, 24h). For expression of the transgene for 3 days, cells were estrogen depleted and the transgene was directly induced for viability purpose.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were pelleted and suspended in Trizol for further RNA isolation.

tag: EREB2-5 cells


title: CAT at 3d, biological replicate 3

description: gene expression data from cells under steady CAT expression for 3 days

source_name: CAT expression 3d


title: EBNA2 at 24h, biological replicate 1

description: gene expression data from cells with 24h EBNA2 expression

source_name: EBNA2 expression 24h


title: CAT at 24h, biological replicate 2


title: EBNA2 at 4h, biological replicate 2

description: gene expression data from cells with 8h EBNA2 expression

source_name: EBNA2 expression 4h


title: CAT at 3d, biological replicate 2


title: EBNA2 at 4h, biological replicate 1


title: EBNA2 at 24h, biological replicate 3


title: CAT at 24h, biological replicate 1


title: CAT at 3d, biological replicate 1


title: EBNA2 at 24h, biological replicate 2


title: EBNA2 at 4h, biological replicate 3


title: CAT at 8h, biological replicate 1

description: gene expression data from cells with 8h CAT expression

source_name: CAT expression 8h


title: CAT at 8h, biological replicate 2


title: CAT at 0h, biological replicate 3

description: gene expression data from cells without induced CAT expression

source_name: CAT expression 0h


title: N2 at 3d, biological replicate 3

description: gene expression data from cells under steady Notch2-IC expression for 3 days

source_name: Notch2-IC expression 3d


title: N2 at 3d, biological replicate 2


title: CAT at 8h, biological replicate 3


title: CAT at 0h, biological replicate 1


title: CAT at 0h, biological replicate 2


title: N2 at 3d, biological replicate 1


title: N2 at 24h, biological replicate 3

description: gene expression data from cells with 24h Notch2-IC expression

source_name: Notch2-IC expression 24h


title: N2 at 24h, biological replicate 2


title: N2 at 8h, biological replicate 3

description: gene expression data from cells with 8h Notch2-IC expression

source_name: Notch2-IC expression 8h


title: N2 at 24h, biological replicate 1


title: N1 at 24h, biological replicate 3

description: gene expression data from cells with 24h Notch1-IC expression

source_name: Notch1-IC expression 24h


title: N2 at 0h, biological replicate 3

description: gene expression data from cells without induced Notch2-IC expression

source_name: Notch2-IC expression 0h


title: N2 at 0h, biological replicate 2


title: N1 at 0h, biological replicate 2

description: gene expression data from cells without induced Notch1-IC expression

source_name: Notch1-IC expression 0h


title: N1 at 8h, biological replicate 3

description: gene expression data from cells with 8h Notch1-IC expression

source_name: Notch1-IC expression 8h


title: N1 at 24h, biological replicate 1


title: N1 at 8h, biological replicate 1


title: N2 at 8h, biological replicate 1


title: N2 at 8h, biological replicate 2


title: N1 at 3d, biological replicate 3

description: gene expression data from cells under steady Notch1-IC expression for 3 days

source_name: Notch1-IC expression 3d


title: N1 at 0h, biological replicate 3


title: N1 at 24h, biological replicate 2


title: embryoid body, microspheres containing Retinoic Acid, 10 days, replicate #3

status: Public on Aug 04 2009

city: Atlanta

first: Nathan

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

description: CEL and CHP files were generated by the Affymetrix Gene Chip Operating System (GCOS) default settings.

hyb_protocol: and hybridized to the Mouse Genome 430 2.0 Array according to manufacturer’s protocols (Affymetrix Inc.).

scan_protocol: scanned according to manufacturer’s protocols (Affymetrix Inc.).

data_processing: CEL and CHP files generated by the Affymetrix Gene Chip Operating System (GCOS) default settings.

label_protocol: Labeled cRNA from three micrograms of total RNA was generated using the One-Cycle Target Labeling and Control Reagents Kit (Affymetrix Inc.)

extract_protocol: Total RNA was extracted from undifferentiated ESCs and EBs using an RNeasy Mini kit (Qiagen Incorporated).

tag: ESCs (D3 line) were maintained in an undifferentiated state on gelatin-coated tissue culture plates in LIF-containing media as described previously.  EBs were formed from 2x106 ESCs inoculated in LIF-free media and cultured under rotary conditions.  EBs containing microspheres were produced by coating CellTracker Red or RA-loaded microspheres in 0.1% gelatin solution for 3 hours prior to mixing with ESCs in various microsphere to cell ratios and a range of rotary speeds.  EB media was exchanged every 1-2 days as needed.